I'm about halfway through reading Hokuto no Ken again (just hit the time skip), and I'd like to provide some points:
After seeing all his fights, I can say Kenshiro is a very serious fighter. He hardly ever goes all out, but he will never fool around or toy with his opponents. Sure, with a common mook, he'll have a dark sense of humor, but he won't smack them around, he one-shots all of them. Depending on Shinobu's personality, he may be slightly lax at first, but he'll get serious right away.
While a lot of Ken's powers are spiritual in nature (his ki, Muso Tensei, etc.), I don't believe that falls under "supernatural," so Shinobu's sword is useless against him.
While Shinobu does have telekinesis, it seems the most powerful thing it's done is crumple an iron door. That's child's play compared to what Kenshiro has endured. Even if he suddenly starts getting thrown around, he's experienced something similar before and can cancel it out by going intangible with Muso Tensei.
According to her profile, Shinobu has really good Regenerationn, recovering from her head being severed and having her limbs ripped off. While Kenshiro usually goes with techniques to make their head explode, once he sees that she can recover from that, he can pull out his techniques that turns the whole body into a red puddle.
By going intangible with Muso Tensei, Kenshiro can erase her existence, which isn't something she should be able to recover from.
Voting Kenshiro for reasons I just listed.